<meta charset="utf8">
<title>Seurat demos</title>

<style>
body{
	padding: 0 10px;
}
hr{
	border: 1px dashed #999;
}

.external_link::before {
    background-color: deeppink;
    content: "->";
    color: white;
}
</style>

<h1>Tutorials about Seurat</h1>




<a href="./seurat_3k_demo.html">seurat_3k_demo.html</a> 基础示例<br>
官网:
	<a class="external_link" target="_blank" href="https://satijalab.org/seurat/">satijalab.org</a> |
	<a class="external_link" target="_blank" href="https://github.com/satijalab/seurat">Github</a> 
<br>

<a href="./sctransform.html">sctransform.html</a> 获取更清晰的生物学差异<br>
<a href="./cell_cycle_vignette.html">cell_cycle_vignette.html</a> 怎么去除细胞周期的变异<br>
<a class="external_link" target="_blank" href="https://zhuanlan.zhihu.com/p/465392721">Seurat 4 R包源码解析》 总目录 | 单细胞转录组分析标准流程@zhihu</a>: 源码解析<br>



<hr>
<a href="./GEO_harmony.html">GEO_harmony.html</a> 导入GEO数据，harmony整合代替PC，用于后续分析 <br>
<a target="_blank" href="https://blog.csdn.net/wangjunliang/article/details/143192137">WNN 多模态整合 | Seurat 单细胞多组学整合流程@csdn</a>: 多模态整合后，可以进行UMAP和细胞聚类。<br>
<a href="./Functions.html">Functions.html</a> Seurat 分析常用函数 <br>







<hr>
<h2>Marker reference</h2>
<a href="./marker_list/index.html">index.html</a> 我的marker基因列表<br>
<a href="./marker_PBMC.html">marker_PBMC.html</a> Azimuth References - Human - PBMC<br>
<a href="./marker_BMMC.html">marker_BMMC.html</a> Azimuth References - Human - Bone Marrow<br>
<a href="./marker_list/mono_macro_DC.html">mono_macro_DC.html</a> 来自网友整理的幕布<br>







<hr>
<h2>单细胞分析包</h2>
<a class="external_link" href="https://www.jianshu.com/p/f8c468b3e97b">monocle2 使用笔记</a> <br>
<a class="external_link" href="https://www.jianshu.com/p/e91b02292bc5">scVelo 的使用: 从bam和Seurat获取输入数据到画图</a> <br>
<a class="external_link" href="https://www.jianshu.com/p/18006139bbed">anndata 数据格式(h5ad 后缀)</a> <br>

<hr>
<a href="./CellChat-vignette.html">CellChat-vignette.html</a> CellChat 单样本示例: https://github.com/sqjin/CellChat/tree/master/tutorial: 2023.6.14<br>







<hr>
<h2>About ML and DL</h2>
<a href="./NMF_demo.html">NMF_demo.html</a> 非负矩阵分解(NMF) 对单细胞分群、降维，十分耗时(1min vs 60min) 2023.9.18<br>

<a href="./cluster_demo.html">cluster_demo.html</a> 机器学习之确定最佳聚类数目的10种方法 2023.9.19<br>









<hr>
<h2>R Extensions</h2>
<a target="_blank" class="external_link" href="https://blog.csdn.net/wangjunliang/article/details/143096799">如何调试该死的Rcpp代码？如何复用Rcpp的so共享库文件？| 向量/矩阵运算@csdn</a>: Rcpp 和 C++ 代码的调试与运行 <br>

















<hr>
notebook版代码库: <a target="_blank" class="external_link" href="https://github.com/DawnEve/scRNAseqCode">scRNAseqCode@github</a>

<hr>
<h2>paper 代码库</h2>
<a href="PubMed/index.html">已发表顶刊的代码</a>
<br>
-- End --
